[English] 日本語
Yorodumi
- PDB-2h2g: The Structural Basis of Sirtuin substrate affinity -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h2g
TitleThe Structural Basis of Sirtuin substrate affinity
Components
  • HISTONE H3 PEPTIDE
  • NAD-dependent deacetylase
KeywordsHYDROLASE / H3-K115AC / SIR2 / SIR2TM / SIRTUIN / SIRT1 / HISTONE H3
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / NAD+ binding ...sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / NAD+ binding / CENP-A containing nucleosome / structural constituent of chromatin / nucleosome / chromatin organization / transferase activity / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Sirtuin, class U / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...Sirtuin, class U / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3 / NAD-dependent protein deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsCosgrove, M.S. / Wolberger, C.
CitationJournal: Biochemistry / Year: 2006
Title: The structural basis of sirtuin substrate affinity
Authors: Cosgrove, M.S. / Bever, K. / Avalos, J.L. / Muhammad, S. / Zhang, X. / Wolberger, C.
History
DepositionMay 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 27, 2012Group: Structure summary
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-dependent deacetylase
B: HISTONE H3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0704
Polymers28,9392
Non-polymers1312
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-31 kcal/mol
Surface area11530 Å2
MethodPISA
2
A: NAD-dependent deacetylase
hetero molecules

B: HISTONE H3 PEPTIDE


Theoretical massNumber of molelcules
Total (without water)29,0704
Polymers28,9392
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area290 Å2
ΔGint-38 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.223, 58.149, 109.062
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NAD-dependent deacetylase / Regulatory protein SIR2 homolog


Mass: 27569.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: npdA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYW0, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide HISTONE H3 PEPTIDE


Mass: 1369.611 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE (YEAST).
References: UniProt: P61830
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 293.15 K / pH: 7.5
Details: 20% PEG, pH 9.6, VAPOR DIFFUSION, HANGING DROP, pH 7.5, temperature 293.15K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 5, 2004
RadiationMonochromator: DIAMOND (111) DOUBLE-CRYSTAL MONOCHROMETER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 37292 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.045 / Net I/σ(I): 27.1
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.409 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / Rfactor Rfree error: 0.005 / SU B: 1.592 / SU ML: 0.057 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: ENGH & HUBER / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1821 4.9 %RANDOM
Rwork0.198 ---
obs0.198 36893 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.9797 Å2 / ksol: 0.540206 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å20 Å20 Å2
2--0.34 Å20 Å2
3----4.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.63→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 2 286 2190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.63→1.73 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 268 4.6 %
Rwork0.245 5606 -
obs--96.3 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more